论文标题
全面评估高通量测序数据的错误校正方法
Comprehensive assessment of error correction methods for high-throughput sequencing data
论文作者
论文摘要
DNA和RNA测序的出现彻底改变了基因组学和分子生物学的研究。下一代测序（NGS）技术，例如Illumina，Ion Torrent，Solid测序等，带来了一种快速，便宜的方法来序列基因组。最近，还开发了第三代测序（TGS）技术（例如PACBIO和牛津纳米孔技术）。不同的技术使用不同的基础方法进行测序，并且容易出现不同的错误率。尽管存在许多工具以纠正NGS和TGS方法的测序数据，但尚无标准方法来评估这些错误校正工具的准确性和有效性。在这项研究中，我们提出了一个针对NGS和TGS平台评估DNA和RNA测序的误差校正方法的核酸序列（Spectacle）的误差校正工具评估的软件包。我们还提出了针对Illumina，PACBIO和ONT平台的测序数据集的汇编，这些数据集呈现出挑战性的错误校正工具方案。使用这些数据集和奇观，我们评估了23种不同的错误纠正工具的性能，并对其优势和劣势提出了独特而有用的见解。我们希望我们的方法论将来将对DNA和RNA误差校正工具的评估进行标准化。
The advent of DNA and RNA sequencing has revolutionized the study of genomics and molecular biology. Next generation sequencing (NGS) technologies like Illumina, Ion Torrent, SOLiD sequencing etc. have brought about a quick and cheap way to sequence genomes. Recently, third generation sequencing (TGS) technologies like PacBio and Oxford Nanopore Technology (ONT) have also been developed. Different technologies use different underlying methods for sequencing and are prone to different error rates. Though many tools exist for error correction of sequencing data from NGS and TGS methods, no standard method is available yet to evaluate the accuracy and effectiveness of these error-correction tools. In this study, we present a Software Package for Error Correction Tool Assessment on nuCLEic acid sequences (SPECTACLE) providing comprehensive algorithms to evaluate error-correction methods for DNA and RNA sequencing, for NGS and TGS platforms. We also present a compilation of sequencing datasets for Illumina, PacBio and ONT platforms that present challenging scenarios for error-correction tools. Using these datasets and SPECTACLE, we evaluate the performance of 23 different error-correction tools and present unique and helpful insights into their strengths and weaknesses. We hope that our methodology will standardize the evaluation of DNA and RNA error-correction tools in the future.
